Contacts of the helix formed by residues 1413 - 1420 (chain H) in PDB entry 6C3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO1413 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1325H TYR 3.3 13.5 - - - +
1326H GLU* 4.8 3.1 - - - -
1327H GLY 3.5 14.3 - - - +
1329H LEU 4.6 10.5 - - - +
1331H PRO* 5.9 6.1 - - + -
1334H ILE* 4.7 6.5 - - + -
1411H LYS 3.8 4.7 - - - +
1412H LEU* 1.3 87.6 - - + +
1414H LEU* 1.3 54.7 + - - +
1415H HIS* 3.1 2.9 - - + +
1416H THR* 2.4 56.1 + - + +
1417H LEU* 2.5 20.4 + - - +
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Residues in contact with LEU1414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323H GLU 3.7 13.2 - - - +
1324H SER* 3.3 26.5 - - - +
1325H TYR* 3.1 22.4 + - + +
1392H PHE 4.7 2.9 - - - +
1393H ARG* 3.6 53.8 - - + +
1412H LEU 3.3 1.9 + - - +
1413H PRO* 1.3 70.8 - - - +
1415H HIS* 1.3 57.2 + - - +
1417H LEU* 3.1 15.4 - - + +
1418H ARG* 2.9 43.2 + - - +
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Residues in contact with HIS1415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513H ALA* 4.1 30.9 + - + +
516H ASN* 5.1 16.9 + - + +
1325H TYR* 4.7 9.7 + - + +
1413H PRO* 3.1 2.9 - - + -
1414H LEU* 1.3 76.9 - - - +
1416H THR* 1.3 62.8 + - + +
1418H ARG 3.9 0.3 - - - -
1419H SER* 2.2 54.1 + - - -
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Residues in contact with THR1416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331H PRO* 6.1 4.9 - - + -
1334H ILE* 5.8 4.0 - - + -
1412H LEU* 4.3 5.9 - - - +
1413H PRO* 2.4 57.4 + - + +
1415H HIS* 1.3 81.9 - - + +
1417H LEU* 1.3 65.0 + - - +
1419H SER* 3.3 7.8 + - - -
1420H ARG* 3.3 45.0 + - - +
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Residues in contact with LEU1417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1391H PHE 3.8 4.5 - - - +
1392H PHE* 3.6 35.9 - - + -
1393H ARG* 3.7 32.1 - - + -
1409H ILE* 3.8 20.2 - - + -
1412H LEU* 4.4 24.0 - - + +
1413H PRO 2.5 17.1 + - - +
1414H LEU* 3.1 23.3 - - + +
1415H HIS 3.1 0.2 - - - -
1416H THR* 1.3 77.5 + - - +
1418H ARG* 1.3 69.6 + - + +
1420H ARG 3.6 0.5 + - - -
1421H LEU* 3.3 31.7 - - + +
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Residues in contact with ARG1418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510H LYS* 2.6 51.9 + - - +
511H LEU* 3.1 23.8 - - - +
512H TYR 4.5 1.4 - - - +
513H ALA* 4.5 9.4 - - + -
1392H PHE* 2.5 50.7 + - + +
1393H ARG* 3.7 3.6 + - - +
1394H MET* 3.1 43.6 - - - +
1414H LEU* 2.9 27.2 + - - +
1417H LEU* 1.3 86.0 - - + +
1419H SER* 1.3 63.9 + - - +
1420H ARG 3.3 0.6 + - - -
1421H LEU 3.6 7.4 + - - +
1497H ARG* 3.5 17.5 + - - -
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Residues in contact with SER1419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512H TYR 5.2 1.1 - - - -
513H ALA* 3.9 9.5 - - - +
1415H HIS* 2.2 48.2 + - - -
1416H THR* 3.7 7.9 - - - -
1417H LEU 3.2 0.2 - - - -
1418H ARG* 1.3 79.7 - - - +
1420H ARG* 1.3 70.6 + - - +
1421H LEU 3.7 1.0 + - - +
1497H ARG* 4.1 16.0 + - - +
1499H THR* 5.4 1.0 - - - +
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Residues in contact with ARG1420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334H ILE* 4.5 20.0 - - - +
1335H PRO 5.1 2.0 + - - -
1336H LYS* 4.6 20.9 + - - +
1338H TRP* 5.3 6.4 - - + +
1339H PRO* 3.9 31.3 - - + +
1416H THR* 3.3 38.0 + - - +
1417H LEU 3.6 0.6 + - - -
1418H ARG 3.3 0.4 - - - -
1419H SER* 1.3 87.2 - - - +
1421H LEU* 1.3 72.3 + - + +
1499H THR* 3.8 18.5 - - - +
1501H ILE* 4.7 2.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il